The map that we see in the game indicates where our characters can travel. Right now. To keep it simple, everyone sees the same map. Regardless of which faction you choose (for example, Klingon or Federation). The map shows Sol (Earth) at its center merely because the majority of the games content is Federation. Hence those circles we see radiating from Sol. As the game updates come to us this might (or might not) evolve the map. Some of those squares (sectors) have been added since the game launched. So it has changed at least once since the game launched.
In the perfect game world, I suppose, each faction would have its own map. With it's own capital at the center. Though none of those Capitols would be in the center of the galaxy itself.